BN9947 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 5 5.2720e-05 6.0652e-03
Layer 6 2.1251e-04 3.2853e-02
Layer 4 2.9750e-04 4.6902e-03
Layer 2 5.9772e-04 7.7075e-02
Layer 3 2.3092e-03 7.0856e-02
WM 3.3304e-02 1.9753e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.2324 0.6816
UBE2QL1 Layer 5 2.0547 0.5872
CHGB Layer 4 1.9941 0.5844
NDRG4 Layer 5 1.9805 0.5625
SLC25A22 Layer 5 1.9902 0.5415
LRPAP1 Layer 5 1.9766 0.5331
PGRMC1 Layer 5 2.0625 0.5330
TOLLIP Layer 4 2.1699 0.5320
SYN2 Layer 5 2.0039 0.5261
PNMA8A Layer 4 2.0840 0.5255
SVOP Layer 5 1.8750 0.5228
MOAP1 Layer 4 1.9189 0.5212
SNAP91 Layer 5 1.8672 0.5209
HPCA Layer 5 2.1055 0.5202
RAN Layer 5 1.9229 0.5199
FAM3C Layer 5 2.1621 0.5196
PHYHIPL Layer 5 1.9629 0.5183
SH3GL2 Layer 5 1.8037 0.5182
NECAP1 Layer 4 1.8750 0.5167
DNAJB6 WM 2.0869 0.5143
IQSEC1 Layer 5 1.9629 0.5133
BMERB1 Layer 5 2.0254 0.5114
SYT4 Layer 5 1.9102 0.5113
COX7A1 Layer 5 1.9189 0.5113
NAP1L5 Layer 5 2.1543 0.5112
NDUFA5 Layer 5 1.8750 0.5109
OXCT1 Layer 5 1.9141 0.5108
STX1A Layer 5 2.0352 0.5104
PCSK1 Layer 5 1.8926 0.5094
YPEL3 Layer 5 1.9014 0.5086
DDX5 WM 2.0146 0.5078
SLC39A10 Layer 5 1.8799 0.5057
HINT3 Layer 5 1.8291 0.5055
GLS Layer 5 1.8623 0.5053
CMAS Layer 5 1.9102 0.5051
FIS1 Layer 4 1.8750 0.5041
CAMK2D Layer 5 2.2578 0.5041
ATP6V1B2 Layer 5 1.8711 0.5033
MAP1LC3A Layer 5 1.9277 0.5032
NAPA Layer 4 1.9453 0.5019
SULT4A1 Layer 4 1.8291 0.5019
EVL Layer 5 1.8799 0.5013
LAMTOR4 Layer 5 1.9229 0.5011
HDGFL3 Layer 5 1.8457 0.5009
ATP6V1A Layer 5 1.9902 0.5008
STMN4 Layer 4 1.9492 0.5007
ITPK1 Layer 4 2.1484 0.5006
ATP6V0D1 Layer 5 2.0039 0.4997
SPRYD3 Layer 4 1.9717 0.4990
PDE1A Layer 5 2.1621 0.4977

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN9947
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN9947_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN9947/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN9947/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN9947/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN9947/report/PD/BN9947_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN9947/report/PD/BN9947_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 11:07:51
  • Number of Processes: 10
  • Spending Time: 0h 3m